Collagen crosslinks are important to the quality of bone and may be contributors to the age-related increase in bone fracture. This study was performed to investigate whether age and gender effects on collagen crosslinks are similar in osteonal and interstitial bone tissues. Forty human cadaveric femurs were collected and divided into two age groups:​ middle-aged (42–63 years of age) and elderly (69–90 years of age) with ten males and ten females in each group (n = 10). Micro-cores of bone tissue from both secondary osteons and interstitial regions in the medial quadrant of the diaphysis were extracted using a custom-modified, computer-controlled milling machine. The bone specimens were then analyzed using high performance liquid chromatography to determine the effects of age and gender on the concentration of mature, enzymatic crosslinks (hydroxylysyl-pyridinoline—HP and lysyl-pyridinoline—LP) and a non-enzymatic crosslink (pentosidine—PE) at these two microstructural sites. The results indicate that age has a significant effect on the concentration of LP and PE, while gender has a significant effect on HP and LP. In addition, the concentration of the crosslinks in the secondary osteons is significantly different from that in the interstitial bone regions. These results suggest that the amount of non-enzymatic crosslinking may increase while that of mature enzymatic crosslinking may decrease with age. Such changes could potentially reduce the inherent quality of the bone tissue in the elderly skeleton.