Delayed and nonunions are still challenging problems. In this study, we examined the endogenous mRNA expression of genes regulating cartilage formation, bone formation, endochondral ossification, and bone remodeling during mechanically induced delayed bone healing in a large animal model. A tibial osteotomy was performed in two groups of sheep and stabilized with either a rigid external fixator leading to standard healing or with a rotationally unstable fixator leading to delayed healing. At days 4, 7, 9, 11, 14, 21, and 42 after surgery, total RNA was extracted from the callus. Gene expressions of several molecules functionally important for bone healing were studied by quantitative reverse transcriptase-polymerase chain reaction. The expression profiles were related to callus tissue composition, analyzed by histomorphometry. Histomorphometry demonstrated a delayed, prolonged chondral phase and a reduction in bone formation in the experimental group. There was no differential expression of Runx2 between both groups until day 42, but mRNA expression levels of BMP2, BMP4, BMP7, noggin, Col1a1, IGF1, TGFbeta1, OPN, MMP9, MMP13, TIMP3, TNFalpha, MCSF, RANKL, and OPG were lower in the delayed healing group at several time points. This study provides insight into the temporal periods during which various factors may be deficient during a compromised bone-healing situation.