Perpetual American Federal Savings, the area's largest thrift institution and frequently an industry pace setter here, will require customers to have at least $50 in their savings accounts beginning Sept. 15. Those who do not will have their accounts closed and the balance refunded by year's end.

The new policy, which affects about 75,000 of Perpetual American's 200,000 passbook and statement savings accounts, reflects a national trend among financial institutions to cut costs by imposing service fees and discouraging small accounts.

Industry officials say those measures are necessary to recapture the cost of servicing savings accounts, an expense that one federal study put at $25.44 a year for an average account.

Notice explaining the new Perpetual American rules are being mailed to customers this month. The only exceptions to the $50 minimum rule will be Christmas savings, telephone bill payer and NOW checking accounts and any account held in the name of a minor under age 18. If a savings account falls below $50 after implementation of the rules, the holder will be given an opportunity to rebuild it before closure.

Typically, lending institutions for years have required minimums of $5 or $10 to open a savings account, but Perpetual appears to be the first in the nation to require as much as a $50 minimum to maintain such an account, according to spokesmen for the U.S. League of Savings Associations and the American Bankers Association.

If Pertual American's particular approach is extraordinary, its cost-cutting intent is not. In general, because these are difficult times for lending institutions, savings and loans in particular, officials "are looking for ways to save money and the cost of small accounts is high," said Patricia Jowers, director of savings accounts for the savings league, a trade association.

The result is that the small saver, who was tolerated by institutions in the past in the hope that he or she would become a big saver, faces shrinking opportunities.

A survey of local institutions, for example, found these practices aimed at trimming the expenses of small accounts:

Minimum of $50 required to open and earn interest on statement and passbook accounts. Such a rule took effect July 1 at Washington Federal Savings & Loan Association, where President James L. Harris said customers can continue to maintain accounts with less than $50 but will not receive any interest until the balance is $50 or more. Exceptions are allowed, however. Interest will be paid on balances of less than $50 for savings in the special accounts for children and Christmas and Hanukah clubs, Harris said.

Minimum of $100 to open a new savings account. First American Bank of Maryland implemented such a requirement on May 1; previously, the minimum was $25. Bank representative Larry Wagaman said that a customer, after opening the account, could maintain the account if the balance fell below $100 and would earn interest on that balance.

Service charges on small accounts. Although savings and loan associations are not allowed to impose service charges on active savings accounts, banks are. Suburban Trust Bank of Maryland, for example, has had a policy since June 30, 1980, of charging $2 for each statement period when the account balance averages less than $100.

From the institutions' point of view, it is all a matter of dollars and cents.

"We are here to make money and our stockholders would not like it if we didn't," said Sharonlee Watkins, advertising manager for Suburban Trust Bank. She said the bank decided to impose service charges because "we had a lot of small accounts that were costing us a lot more than the income we were getting from them."

For the individual saver, the rule changes demand special care or a change in saving strategy. In the past, a person typically could deposit funds in a traditional savings account and earn the standard rate of interest on his or her money. But that frequently is not the case anymore.

Service charges and interest penalities tied to the account balance or to the number of withdrawals made during the quarter can substantially reduce the amount of interest that the person otherwise would collect. Such losses can be particularly painful for individuals who learn too late that they would not have been penalized if their money had been in another type of account.

Consider the case of Guy C. Thomas, Jr., an enterprising 16-year-old who lives in Oakton, Va., with his family.

Last summer Thomas earned nearly $3,000 from a paper route and odd jobs. He deposited most of the money in a savings acount so that it could earn interest until he needed to withdraw it during the school year. But when the bank statement for the quarter ending March 31 arrived, Thomas found that his account, which had fallen steadily but never went below $1,600, had earned less than $5 interest.

The teen-ager had been paid 1 percent interest instead of the bank's standard 5.25 percent because of a penalty on too many withdrawals.

"They showed me the fine print" spelling out the rule, Guy C. Thomas Sr. said. And, indeed, there had been 10 withdrawals during the quarter; the bank rules allowed two without penalty on a balance of less than $2,000.

Shirley Beavers, senior vice president at First Virginia Bank, where young Thomas had his account, said the youth could have avoided the penalty if he had his money in a special interest-bearing checking account rather than the regular savings account. Thomas did that several weeks after he realized there was an alternative for savers with comparatively high-average account balances. The special account, for example, is not subject to the $3-a-month service charge so long as the average monthly balance does not drop below $1,000. The account pays 5.25 percent interest and allows unlimited withdrawals.

None of the institutional rules is engraved in cement, however.

Some are repealed when they don't work out or when the economic climate shifts. First Virginia, for example, will drop the penalty that cost young Thomas and allow unlimited withdrawals on savings accounts beginning Oct. 1, Beavers said, because "we need the small saver and the small save who can't qualify for money market funds still needs that kind of account."

More rules are apt to change in the future as institutions experiment, searching for the best ways to attract bigger accounts and to minimize the costs of the small ones.

"They are all looking at their administrative costs . . . at the cost of keeping books," said Jim Christian, chief economist for the U.S. League of Savings Association.

In addition to each institution's examination of internal cost, the industry as a whole is trying to identify expenses. The American Bankers Association, for example, is conducting a survey that asks questions about a host of costs -- including the expense of maintaining a savings account.

The latest information now available comes from the government study that found that it cost $25.44 a year to service the average account. The study, conducted by the Federal Reserve System for the year 1979, showed that the average savings account had a balance of $1,903 and cost the medium-size bank $2.36 for handling deposits, $3.45 for handling withdrawals, 55 cents for opening accounts, 29 cents for closing accounts, $6.87 for posting interest and $11.92 for annual account maintenance including postage and paper for mailing out statements.

Institutions making changes sometimes play down the significance of the shift. Perpetual American's Owen, for example, said his S&L's $50 minimum for maintaining an account affects less than 1 percent of deposits and is not really anything new, pointing to American Security Bank's practice of discouraging small savings accounts by imposing service charges.

Since 1978, American Security has charged $1 a month when the balance in the savings account fell below $200. Some local institutions have had minimum balance rules even longer than that. Home Federal Savings and Loan Association, for example, has had a policy since 1973 of refusing to pay interest on savings accounts containing less than $50.

Now those practices are spreading. And the prediction from many savings officials is that they will continue to spread in the months ahead.

"You can't turn off the small saver, but on the other hand, you can't offer a product that you know is losing money," said Glenn L. Schickler, vice president of Madison National Bank. "Supermarkets can do that -- lose money -- on one item because with 10,000 items they can make it up somewhere else in their stores. But a bank has only three or four services -- checking, savings, loans, safety deposit boxes -- and you can't have two of those four as loss leaders."