Partially reprogrammed cells [preinduced pluripotent stem cells (pre-iPSCs)] commonly stall at epigenetic barriers, and this is one of the major failures in the reprogramming process. These cells can be converted to the fully reprogrammed state by reducing epigenetic blocks. In this study, we established three iPSC lines and two pre-iPSC lines induced by the doxycycline (dox)-inducible lentiviral system. In the pre-iPSC lines maintained under dox treatment (dox(+)), a small portion of embryonic stem cell (ESC)-like colonies spontaneously emerged after dox withdrawal (dox(-)), and major differentiation into fibroblast-like cells occurred. The spontaneous conversions based on the number of stage-specific embryonic antigen-1-positive (SSEA-1(+)) colonies were 0.006 ± 0.004% [mean ± standard deviation (SD)] for the #89-7D line and 0.016 ± 0.004% for the #102-2D line. The SSEA-1(+) colonies did not express the Nanog protein. However, the colonies showed characteristics typical of fully reprogrammed iPSCs after further expansion. To determine whether spontaneous conversion could be improved by epigenetic modification, we applied four small molecules-valproic acid (VPA), sodium butyrate (SB), trichostatin (TSA), and 5-aza-2'-deoxycytidine (5-Aza)-in both pre-iPSC lines. SB was the most effective molecule in enhancing the number of SSEA-1(+) colonies (32- to 39-fold) at day 5 of dox(-) treatment. In addition, the expression of pluripotent genes (sox2 and nanog) was increased by SB. After exposure to SB, we found that the expression of four reprogramming factors and cell cycle-related genes was relatively increased compared to their expression following dox(+) of pre-iPSCs. These changes caused by SB might play an important role in the spontaneous conversion of partially reprogrammed cells.