Background: In primary care 15% of patient encounters are perceived as challenging by general practitioners (GP). However it is unknown what impact these encounters have regarding job satisfaction. The aim of this study was to evaluate which encounters are perceived as challenging by German GPs and whether they were associated with job satisfaction. Methods: A total of 1538 questionnaires were sent to GPs in the federal state of Schleswig-Holstein, Germany. GPs should rate 14 medical conditions and 8 traits of patients on the perceived challenge using a Likert scale (1: 'not challenging at all' to 10: 'extremely challenging'). Job satisfaction was measured with the Warr-Cook-Wall job satisfaction scale. A linear regression analyses were used to explore potential associations between for the primary outcome variable 'overall job satisfaction'. Results: Total response was 578 (38%). GPs perceived 16% of their patients as challenging. Psychiatric disorders such as somatization disorder (mean = 7.42), schizophrenia (mean = 6.83) and anxiety disorder (mean = 6.57) were ranked as high challenging while diabetes mellitus type 2 (mean = 4.87) and high blood pressure (mean = 3.22) were ranked as a rather low challenging condition. GPs were mostly satisfied with 'colleagues' (mean = 5.80) and mostly dissatisfied with their 'hours of work' (mean = 4.20). The linear regression analysis showed no association with challenging medical conditions and traits of patients but only with different aspects of job satisfaction concerning the outcome variable 'overall job satisfaction'. Conclusions: Especially psychiatric conditions are perceived as challenging the question arises, in what amount psychiatric competences are gained during the postgraduate specialty training in general practice and if GPs with a mandatory rotation in psychiatry perceive these conditions as less challenging. Interestingly this study indicates that challenging encounter in terms of challenging medical conditions and traits of patients do not affect GP's job satisfaction.