Condom compatible lubricants (CCLs), including water-based lubricants (WBL) represent one strategy to prevent the breakage of latex condoms and thus decrease the risk of HIV transmission during anal intercourse. The analyses presented here characterize the correlates of WBL use during anal sex among men who have sex with men (MSM) in Blantyre, Malawi enrolled from April 2011 to March 2012 using respondent-driven sampling (RDS). Bivariate and multivariable logistic regression analyses with RDS-weighting were conducted on a total sample of 338 MSM. With RDS-weighting, 25.4% [95% confidence interval (CI): 20.3-31.4] of MSM (106/329) reported primarily using WBL during anal sex. In multivariable analysis, higher income [adjusted odds ratio (aOR): 5.9; 95% CI: 2.48-14.19], family being aware of their sexual practices (aOR: 2.52; 95% CI: 1.29-4.92), and reporting consistent condom use in the last 6 months (aOR: 1.27; 95% CI: 1.06-1.52) were positively associated with WBL use. Increasing age (per 1 year increase in age; aOR: 0.89; 95% CI: 0.83-0.95) was negatively associated with WBL. Taken together, these data highlight the limited uptake of WBL among MSM in Blantyre, Malawi, especially among older men and those belonging with lower income. Older MSM in Malawi are known to have a higher prevalence of HIV and lower reported use of WBL, suggesting significant risks of onward HIV transmission. Separately, the limited use among those with lower incomes suggests the need for free or subsidized distribution of CCL together with condoms and counseling about their use specifically for MSM in Malawi.