We aimed to describe health seeking and sexual behaviour including condom use among patients presenting with sexually transmitted infections (STI) and, to identify socio-demographic and behavioural risk factors associated with "no condom use" during the symptomatic period. A cross-sectional study of consecutive new STI cases presenting at the district STI clinic in Thyolo were interviewed by STI counsellors after obtaining informed consent. All patients were treated according to National guidelines. Of 498 new STI clients, 53% had taken some form of medication before coming to the STI clinic, the most frequent alternative source being the traditional healer (37%). 46% of all clients reported sex during the symptomatic period (median=14 days), the majority (74%) not using condoms. 90% of all those who had not used condoms resided in villages and had seen only the traditional healer. Significant risk factors associated with "no condom use" included: visiting a traditional healer; being female; having less than 8 years of school education; and being resident in villages. Genital ulcer disease (GUD) was the most common STI in males (49%) while in females this comprised 27% of STIs. These findings, especially the extremely high GUD prevalence is of particular concern, considering the high national HIV prevalence in Malawi (9%) and the implications for STI and HIV transmission. There is an urgent need to integrate traditional healers in control activities, encourage their role in promoting safer sexual behaviour, and to reorient or even change existing strategies on condom promotion and STI control.