Aims Journal impact factors (IMFs) are used increasingly by institutions as performance indicators of the quality of 'individual research output'. Although the need for discretion when using the numbers has been emphasized, there has been little formal analysis of the issues. We therefore investigated citation profiles for three clinical pharmacology journals to assess the validity of using IMF as a measure of 'individual research'. Methods We compared the pattern of individual citations for random samples of 120 papers published in Clin Pharmacol Ther (CPT), Br J Clin Pharmacol (BJCP) and Eur J Clin Pharmacol (EJCP) in 1981, 1991, 1995 and 1996. Using an analogy between citation-time profiles of papers and concentration-time profiles of drugs, it was possible to define 'lag-time', C-max, t(max), t(1/2) and AUC(t), and to investigate 'bioequivalence'. Results Citation distributions for individual publications were widely variable and skewed (skewness = 1.47, 2.16 and 1.37 for CPT, BJCP and EJCP, respectively). The 90% CI values for the IMF of a publication in each journal (i.e. 90% CI for an observation as opposed to 90% CI for the mean) were 0.24-16.94, 0.08-10.3 and 0.09-5.68. Conclusions IMF does not represent the impact of an individual paper. Furthermore, if the comparison of journals is treated as a bioequivalence issue, the citation data should be log transformed prior to calculating IMF such that they represent the likelihood of citation for the median article. After such transformation, absolute differences between the IMF of clinical pharmacology journals become much smaller.