For better fixation, formalin injection of radical prostatectomy (RP) specimens has been suggested. We aimed to assess its effect on immunoreactivity using immunohistochemistry (IHC). A tissue microarray of cancer and benign tissues from 42 RP specimens was constructed. Twenty-one of the prostates had been injected with formalin prior to formalin immersion. IHC staining was performed using 15 antibodies, including nuclear and cytoplasmic markers known to be positive in prostate tissue: pan cytokeratin, P504S, high molecular weight (HMW) keratin, PSA, vimentin, actin HHF35, thioredoxin-1, peroxiredoxin-2, PDX-1, BAX, p27, androgen receptor (AR) and heat shock proteins (HSP) 27, 60 and 70. Differences in staining intensity in cancer and benign tissues were compared separately except for HMW keratin. Only 7 of 29 analyses showed significant differences between groups, including 5 of 15 antibodies. The expression of AR and HSP 27 was stronger in formalin-injected tissue, while the opposite was true for HSP 60, HSP 70 and peroxiredoxin-2. For most antibodies, formalin injection does not significantly affect immunoreactivity in prostate tissue. The staining variability caused by inter- and intratumoral heterogeneity may be greater than that caused by the fixation method.