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.

Payments have been stopped to the West London Vocational Training College and its students in the Welsh capital.
Education Minister Huw Lewis said there were concerns over "unusual student recruitment trends".
The college said as far as it is concerned, all of its students are genuine.
The Cardiff branch runs various IT and business courses and has been designated as suitable to offer HND business courses, which attract tuition fees of Â£6,000 per student, funded by the Welsh government.
Students on those courses can also apply for Student Finance Wales loans and grants.
Week In Week Out has been investigating offers made by a local agent recruiting for the college.
Some students have been told by him they can use faked documents to access those loans and grants and they do not have to attend regularly to get the cash.
He also said if they do not go on to earn more than Â£21,000, they will not have to repay the money - which is true.
The college has denied any knowledge of that scam.
In a statement to AMs on Friday, Mr Lewis said: "Allegations have since come to light to suggest that one or more individuals within the college may have colluded with prospective students deliberately to defraud the student finance system by falsifying academic records and records of attendance at the college.
"I would expect any allegations of criminal activity to be referred to the police so that they may be investigated fully."
Pearson UK - which validates colleges - carried out a review of the Cardiff campus, visiting the site on 21 October.
The education minister said that "no substantive concerns came to light at that time".

Ogwen Valley Mountain Rescue team was called to Yr Elen, in the Carneddau range, at about 14:00 GMT on Saturday.
The man, who had rib and back injuries, was flown to hospital in a rescue helicopter.

De Roon moved to Teesside in June 2016 for an initial £8.8m fee and played 33 Premier League games last term.
The Netherlands international, 26, scored five goals in 36 league and cup games during his spell at Boro.
Meanwhile, manager Garry Monk confirmed the Championship club's interest in signing Chelsea midfielder Lewis Baker.
"He's a target and one of many that we've had throughout the summer months," said Monk.
Find all the latest football transfers on our dedicated page.
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.
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Payments to a college's Cardiff campus have been suspended after a BBC Wales' Week in Week Out investigation into fraud allegations.
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A man in his 60s has been airlifted to hospital after falling while walking in Snowdonia.
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Italian Serie A side Atalanta have re-signed midfielder Marten De Roon from Middlesbrough for an undisclosed fee, 14 months after selling him to Boro.