Research biopsies have great potential to advance scientific knowledge by helping to establish predictors of favourable or unfavourable outcomes in kidney transplantation. We evaluated punch and core biopsies of different sizes to determine the optimal size for clinical use. A total of 54 punch biopsies and 18 core needle biopsies were retrieved by three transplant surgeons. Each surgeon obtained three separate 2mm, 3mm and 4mm punch biopsy samples and three 23mm (length) core needle biopsies from two pig kidneys. 4mm punch biopsies yielded the greatest amount of protein (2.11 ± 0.41mg) with good reproducibility between surgeons and biopsy types (Coefficient of Variation ∼ 22.13%). All surgeons found 2mm biopsies technically challenging to obtain and sample processing was difficult due to the sample size. Shotgun proteomics identified 3853 gene products with no significant difference in the quantitative proteome of 2mm and 3mm punch biopsies. However, the expression of 158 Kidney enriched genes, was higher in bigger and deeper 4mm punch and core needle biopsies compared to 2mm biopsy. Only 80% of 2mm biopsies demonstrated the presence of glomeruli, whereas glomeruli were present in 100% of all other biopsy sizes. The 2mm punch biopsy has been shown to be challenging to use and frequently provides inadequate tissue for histology and proteomics while 3mm research biopsies were the smallest size that were technically obtainable with adequate tissue for molecular studies.