Induced pluripotent stem cell (iPSC) derived cardiomyocytes are an important model system for cardiac electrical disorders. They offer the potential to detect disease-specific differences in cell lines as well as between healthy individuals of differing genetic backgrounds. However, variability of iPSC cardiomyocyte differentiations makes these studies prone to type 1 errors and optimal experimental designs and sample sizes remain undefined. We aimed to characterise the variability in electrical properties of cardiac myocytes derived from three iPSC lines obtained from healthy individuals, at baseline, in response to varying pacing rates and in the presence of two pharmacological challenges to repolarisation reserve: inhibition of IKr and augmentation of INaL. We aimed to explore the mechanisms underlying the variability in iPSC-derived cardiomyocyte phenotypes by analysing transcriptional profiles. Four replicate cardiomyocyte differentiations from three iPSC lines were analysed on 48-well multielectrode arrays (MEA). Field potential recordings were made from spontaneous beating monolayers as well as during pacing at 0.5, 1.0 and 1.5 Hz at baseline and in the presence of dofetilide (10 nM) and ATX II (25 nM). Field potential parameters were correlated with mRNA levels for a panel of 48 transcripts of key cardiac ion channel, calcium handling, sarcomeric and metabolic genes, assayed using the NanoStrings platform. Significant variability in baseline field potential parameters was observed between replicate differentiations of each line, whereas differences between iPSC lines were not statistically significant in nested ANOVA and mixed effects model analyses after taking into account within line variability. The rate-dependence of repolarisation and repolarisation reserve also showed significant intra-line differences but again interline differences were not significant. Field potential durations showed the strongest correlation with expression of two sarcomeric genes, MYH2 and MYH7. Significant variability in phenotypes between replicate differentiations of the same iPSC line indicates that a large number of replicates are needed in studies designed to detect differences between lines derived from healthy individuals. One should also take this into account when comparing diseased lines with isogenic controls. Maturation state and cardiomyocyte purity of differentiations are an important cause of variability in MEA field potential recordings.