Standards in the use of statistics in medical research are generally low. A growing body of literature points to persistent statistical errors, flaws and deficiencies in most medical journals. In this paper we present a comprehensive review of common statistical pitfalls which can occur at different stages in the scientific research process, ranging from planning a study, through conducting statistical data analysis and documenting statistical methods applied, to the presentation of study data and interpretation of study results. 47 potential statistical errors and shortcomings, differentiated for the distinct phases of medical research are presented and discussed. Statisticians should be involved early in study design, as mistakes at this point can have major repercussions, negatively affecting all subsequent stages of medical research. Consideration of issues discussed in this paper, when planning, conducting and preparing medical research manuscripts, should help further enhance statistical quality in medical journals.