Background To understand longitudinal trends in sexually transmitted infection (STI) syndromes, we conducted a descriptive analysis of syndromic STI diagnoses at an STI clinic in Lilongwe, Malawi over the last 5 years. Methods Using data collected routinely at all STI clinic visits since March 2006, we calculated the proportion of patients seen in each of the last five calendar years (2006, 2007, 2008, 2009, and 2010) who were diagnosed with each of the following STI syndromes—genital ulcer disease, genital warts, abnormal vaginal discharge (females), lower abdominal pain (females), urethral discharge (males), balanitis (males), swollen inguinal lymph nodes (males), and scrotal swelling (males). Results An average of 6694 unique patients were seen each year; approximately 60% were female and 40% were male. Among males, the most common diagnoses were urethral discharge, genital ulcer disease, and balanatis (Abstract P1-S1.24 figure 1). There was an increase in the prevalence of urethral discharge over the period 2006–2010 (from 28% to 33%, p<0.0001), but there was a slight decrease in the prevalence of genital ulcer disease (from 22% to 20%, p=0.02) and balanitis (from 13.5% to 12%, p=0.0002). Among females, the most common diagnoses were abnormal vaginal discharge, lower abdominal pain, and genital ulcer disease. There was an increase in the prevalence of abnormal vaginal discharge over the period 2006–2010 (from 40% to 45%, p<0.0001), but there was a decrease in the prevalence of lower abdominal pain (from 50% to 33%, p<0.0001) and genital ulcer disease (from 13% to 10%, p<0.0001). The prevalence of all other STI syndromes remained below 10% throughout the study period. Abstract P1-S1.24 Figure 1 Syndromic STI prevalence and 95% CI, Kamuzu Central Hospital STI Clinic, Lilongwe, Malawi, 2006–2010. LAP, lower abdominal pain; AVD, abnormal vaginal discharge; UD, urethral discharge; GUD, genital ulcer disease; BA, balanitis; F, female; M, male. Conclusions Urethral discharge and balanitis continue to be highly prevalent among males; abnormal vaginal discharge and lower abdominal pain continue to be highly prevalent among females; and genital ulcer disease continues at a high prevalence in both groups. Of note, the decline in lower abdominal pain coincides with a documented drop in cases of gonorrhoea and chlamydial infection in this population, and the small decline in genital ulcer disease may be due to recent improvements in chancroid treatment. The very high prevalence of urethral discharge among men and abnormal vaginal discharge among women may be due in part to observed high levels of trichomoniasis in this population, and the increases in these diagnoses suggest that trichomoniasis prevalence may be on the rise.