Cultivation of neonatal mouse testis tissue can induce spermatogenesis and produce fertile sperms. However, in vitro spermatogenesis mediated by the current organ culture method comes short in fully mimicking the in vivo counterpart, partly due to a lack of knowledge underlying molecular phenotypes of in vitro spermatogenesis. In this study, we investigated transcriptome of cultured testis tissues using microarray method. Principle component analysis of the transcriptome data revealed delay and/or arrest of spermatogenesis and immediate radical immune reactions in the cultured testis tissues. The delay/ arrest of spermatogenesis occurred before and during early meiotic phase, resulting in inefficient progression of meiosis. The immune reaction, on the other hand, was drastic and overwhelming, in which TLR4-NF-kB signaling was speculated to be involved. Notably, treatment with TAK242, an inhibitor of TLR4-NF-kB signaling pathway, ameliorated the macrophage activation which otherwise would exacerbate the inflammation. Thus, the present study revealed for the first time at molecular level that the deficiency of germ cell differentiation and the immense immune reaction are major abnormalities in the cultured testis tissues. (c) 2020 The Authors. Published by Elsevier Inc.