Relief at last.

There are now toilet seats in city subway bathroom stalls — after the MTA landed in deep doo-doo with the agency’s Inspector General’s Office, which told it to get off the pot and install them.

“I’m pleased that New York City transit agreed with our recommendations and is taking steps that will make these bathrooms easier to locate and more comfortable to use,” said MTA Inspector General Daniel Cort in a statement.

“Small fixes – like adding toilet seats – can make a big difference in comfort and hygiene for riders.”

After issuing a scathing report on the issue earlier this year, Cort’s office said it recently found new black or white seats for toilets at the 161st Street-Yankee Stadium station (B, D and 4 lines) and Pelham Bay Park (6 line) in The Bronx.

New toilet seats also have been installed in restrooms in Manhattan’s 14th Street Union Square station (L, N, Q, R, W, 4,5 and 6), 125th Street station (A,B,C,D), 168th Street station (A,C and 1), Inwood- 207th Street station (A ).

Seats were put in the following Queens station, as wells: Jackson Heights-Roosevelt Avenue (E,F, M, R and 7), Queensboro Plaza (N, W and 7), Main Street (7 line) in Flushing, Mets-Willets Point (7), Forest Hills (E, F, M and R), Kew Gardens (E,F), 179th Street (F), and Jamaica Center Parsons-Archer (E, J and Z).

In most cases, the replacements occurred in both men’s and women’s bathrooms.

MTA/NYC Transit said in a response to the MTA IG’s audit in February that it would “explore installing seats on existing toilets that can accommodate them without requiring retrofitting or significant structural modifications.”

The good news is that NYC Transit kept its promise, according to the IG.

The same earlier audit also found some of the public restrooms in skeevy conditions, lacking the basics such as toilet paper, soap and garbage cans and secure locks.

Transit officials said they sent instructions to their cleaners to improve bathroom upkeep.