The association and groups including the Mountaineering Council of Scotland have raised concerns in the past about rubbish being left in the shelters.
Use of bothies increases in summer months.
The MBA has now issued a new message asking people to help keep bothies in a tidy state.
The association said: "With summer upon us we are seeing many visitors to bothies, especially on the more popular long-distance trails, who perhaps have not used one before and who seem unaware that unlike in some other countries, our mountain bothies are not serviced and have no rubbish collection service.
"Bothies rely on you to remove your litter, and that of any inconsiderate others, so please help where you can."
Last year, one of two volunteers who looks after Corrour Bothy in the Lairig Ghru, Cairngorms, told of taking four hours to sort through and burn waste left there.
Neil Reid said hillwalkers had to be willing to pick up litter they find.
The Mountain Bothies Association has appealed to hillwalkers and climbers to help keep more than 100 shelters it looks after in the UK clean and tidy.