Background Main sexual partners are an important source of new HIV infections among MSM. Additionally, receptive (compared with insertive) anal intercourse carries considerably greater risk of HIV transmission. We investigated younger MSM’s (YMSM, aged 16–29) condom use in New Zealand by main partner type and anal modality.

Methods The study included 1,221 YMSM who reported anal intercourse with a main partner (boyfriend or fuckbuddy) in the last six months from 2006, 2008 and 2011 rounds of the Gay Auckland Periodic Sex Survey and Gay men’s Online Sex Survey. Condom use for both receptive and insertive anal intercourse was categorised into three levels: high (always/almost always), medium (about half the time), or low (very rarely/never). Associated factors were identified with four backward stepwise multivariate multinomial logistic regression models retaining at p < 0.05.

Results The majority of YMSM classified their main regular partner as a boyfriend (59.5%). Overall, high condom use (receptive and insertive) was more likely with a fuckbuddy (59.2% and 59.4%) than a boyfriend (35.8% and 37.5%). Condom use was lower among YMSM in a relationship longer than one year, and was more common among those who used them more with casual partners. YMSM who only had insertive anal intercourse with their boyfriend were more likely to report high condom use compared with YMSM who also had receptive anal intercourse. However, compared with YMSM who were both insertive and receptive with casual partners, YMSM who were exclusively insertive with casual partners were less likely to report high condom use during insertive anal intercourse their boyfriend. YMSM who believed condoms reduce sensitivity were less likely to report using condoms.

Conclusion Condoms remain the leading STI primary prevention tool for sexually active YMSM. Sexual health education to improve condom use and discussions about extra-relational sex should be provided with consideration to anal modality.