Syphilis has been reinstated on the list of notifiable diseases in Switzerland since 2006 and the active management of sexual partners is encouraged to avoid reinfection. However, contact tracing has yielded unsatisfactory results and the incidence of syphilis remains important, especially in high-risk populations. The aim of this study was to compare the proportions of notified sexual partners of patients diagnosed with syphilis by the laboratories of Geneva University Hospitals (HUG) with those diagnosed in private laboratories (non-HUG) and to assess the risk factors for no notification to sexual partners. All syphilis cases notified to the Office of the Surgeon General in Geneva (Switzerland) between 1 January 2011 and 31 December 2013 were analysed. The proportions of partner notification (PN) between HUG and non-HUG laboratories were compared by Chi square test and the main risk factors for no notification to sexual partners were assessed by binomial log-linear regression. Among a total of 720 notifications reported, 244 cases were diagnosed with contagious syphilis stages and 263 with non-contagious stages (i.e. successfully treated patients with or late latent cases). Overall, PN was higher among contagious than non-contagious cases (58.4% versus 31.0%; p = 0.030) and it was significantly higher in the non-HUG compared to the HUG group (75.9% versus 50.0%, respectively; p < 0.001). Risk factors independently associated with no notification to sexual partners were the place of diagnosis (risk ratio [RR] 1.66; 95% confidence interval [CI] 1.21-2.27 for HUG versus non-HUG, respectively), age >45 years (RR 1.36; 95% CI: 1.05-1.76) and if the patient had received treatment for syphilis (RR 1.91; 95% CI: 1.38-2.66). Our results illustrate the difficulty of contact tracing in syphilis infection and the necessity to improve this crucial part of sexually transmitted infection management.