The validity of a systematic review depends on completeness of identifying randomised clinical trials (RCTs) and the quality of the included RCTs. The aim of this study was to analyse the effects of hand search on the number of identified RCTs and of four quality lists on the outcome of quality assessment of RCTs evaluating the effect of physical therapy on temporomandibular disorders. In addition, we investigated the association between publication year and the methodological quality of these RCTs. Cochrane, Medline and Embase databases were searched electronically. The references of the included studies were checked for additional trials. Studies not electronically identified were labelled as "obtained by means of hand search". The included RCTs (69) concerning physical therapy for temporomandibular disorders were assessed using four different quality lists: the Delphi list, the Jadad list, the Megens & Harris list and the Risk of Bias list. The association between the quality scores and the year of publication were calculated. After electronic database search, hand search resulted in an additional 17 RCTs (25%). The mean quality score of the RCTs, expressed as a percentage of the maximum score, was low to moderate and varied from 35.1% for the Delphi list to 54.3% for the Risk of Bias list. The agreement among the four quality assessment lists, calculated by the Interclass Correlation Coefficient, was 0.603 (95% CI, 0.389; 0.749). The Delphi list scored significantly lower than the other lists. The Risk of Bias list scored significantly higher than the Jadad list. A moderate association was found between year of publication and scores on the Delphi list (r = 0.50), the Jadad list (r = 0.33) and the Megens & Harris list (r = 0.43).