We aimed to detect truncated CCN3 protein variants in formalin-fixed paraffin-embedded samples of eight Wilms’ tumors using anti-K19M and novel domain-specific antibodies, anti-NH2, anti-NH3, anti-NH4, and anti-NH5 raised against C-terminal (CT) domain and modules 1, 2, 3, and 4 of the CCN3 protein, respectively. In Wilms’ tumors, all the domain antibodies except anti-NH4 exhibited both nuclear and cytoplasmic staining in blastema as well as primitive tubules. NH4 was detected only in the cytoplasm of tumor cells. Normal fetal kidneys revealed mainly cytoplasmic immunoreactivity for all antibodies in tubules and glomeruli, except for K19 and NH5, which showed some nuclear staining. Our data suggest expression of a truncated nuclear CCN3 variant lacking the thrombospondin type-1-like domain and cytoplasmic full-length CCN3 protein in Wilms’ tumor cells. In addition, normal fetal kidneys express mainly full-length protein mostly localized to cytoplasm. Truncated CCN3 protein in Wilms’ tumor cells may provide evidence for its tumorigenic role in these tumors. Uniform NH5 staining compared to variable expression of K19M indicates that using NH5 is a better approach for detecting the CT domain of CCN3 protein in archival specimens. Thus, the domain-specific antibodies represent valuable tools for detecting CCN3 protein variants in normal and neoplastic kidneys.