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Objective: Auto-regeneration of the intestinal and ovarian tissue are experiencing degenerative due to protein energy malnutrition (PEM) through of auto-mobilization, increase of immune response and differentiation of endogenous stem cells. Methods: Female rat model of PEM obtained through fasting meals for 5 d and only to drink, causing malnutrition and damage of the intestinal and ovarian tissue. Furthermore, the therapy of honey with a dose of 30% water (T1) and 50% water (T2) respectively for 5 d and compared with the positive control, were fasted without being given honey (T0+) and negative control, not fasted and without being given honey (T0-). Observations on: auto-mobilization, increased immune response, differentiation of stem cells, and regeneration of the intestinal and ovarian tissue with HE staining. Results: Auto-mobilization of stem cells based on the expression of CD34+ and CD45+, which is a marker of endogenous stem cells (haematophoeietic stem cells/HSCs). Increased immune response is based on Hsp70 expression and PGE2 in intestinal tissue. Differentiation of stem cells into progenitor cells that expected based expression of growth differentiation factor-9 (GDF-9) by immunohistochemistry in ovarian tissue. Conclusions: Expression of CD34+ and CD45+, which significantly different in treatment 2 (2). Furthermore, increase of immune response (decrease Hsp70 expression and increased PGE2) in intestinal tissue. Increased immune response causes expression of GDF-9 in ovarian tissue. Decreased of Hsp70 expression, increased PGE2 and increased GDF-9 followed the process of regeneration of the intestinal and ovarian tissue.