Background: Publication bias is an important factor that may result in selection bias and lead to overestimation of the intervention effect. In this study, the focus was on using capture-recapture method as a statistical procedure which may possibly be a practical means for measuring the amount of publication bias. Methods: A systematic review was conducted to estimate the duration of protection provided by hepatitis B vaccine by measuring the anamnestic immune response to booster doses of vaccine and retrieved studies from three separate sources of electronic databases, reference lists of the studies, and conference databases as well as contact with experts and manufacturers. Capture-recapture and some conventional methods such as funnel plot, Begg test, Egger test, and trim and fill method were employed for assessing publication bias. Results: Based on capture-recapture method, completeness of the overall search results was 87.2% [95% CI: 84.6% to 89.0%] and log-linear model suggested 5 [95% CI: 4.2 to 6.2] missing studies. The funnel plot was asymmetric while Begg and Egger tests results were statistically insignificant and trill and fill approach made no change in pooled effect. Conclusions: Capture-recapture method may be a useful practical approach for estimating the number of missing studies which are not usually detected by search strategy. As a result, use of capture-recapture method as an alternative approach could be suggested for estimating the extent of publication bias based on overlapping information rather than mirror image of extreme values on funnel plot.