Magnetic resonance images (MRI) require intensity standardisation if they are used for the purpose of quantitative analysis as inherent variations in image intensity levels between different image sets are manifest due to technical factors. One approach is to standardise the image intensity values using a statistically applied biological reference tissue. The aim of this study is to compare the performance of differing candidate biological reference tissues for standardising T2WI intensity distributions. Fifty-one prostate cancer patients across two centres with different scanners were evaluated using the percentage interpatient coefficient of variation (%interCV) for four different biological references; femoral bone marrow, ischioanal fossa, obturator-internus muscle and bladder urine. The tissue with the highest reproducibility (lowest %interCV) in both centres was used for intensity standardisation of prostate T2WI using three different statistical measures (mean, Z-score, median + Interquartile Range). The performance of different standardisation methods was evaluated from the assessment of image intensity histograms and the percentage normalised root mean square error (%NRSME) of the healthy peripheral zone tissue. Ischioanal fossa as a reference tissue demonstrated the highest reproducibility with %interCV of 18.9 for centre1 and 11.2 for centre2. Using ischioanal fossa for statistical intensity standardisation and the median + Interquartile Range method demonstrated the lowest %NRMSE across centres for healthy peripheral zone tissues. This study demonstrates ischioanal fossa as a preferred reference tissue for standardising intensity values from T2WI of the prostate. Subsequent image standardisation using the median + Interquartile Range intensity of the reference tissue demonstrated a robust and reliable standardisation method for quantitative image assessment.