Neanderthal femora exhibit documented morphological differences compared to those of other Homo [1-2], including Homo sapiens, particularly in the internal structure of their diaphysis. However, comprehending the intra-specific diversity of femoral structure among Neanderthals is crucial for elucidating the broader diversity within the Homo genus throughout the Middle and Late Pleistocene. This study aims to comprehensively document the diversity of femoral structure among Neanderthals, both chronologically and geographically. We conducted an analysis of the internal structure of femoral diaphyses of Neanderthal individuals from the Levant and Northern, Central, and Western Europe. The study incorporates both previously published and newly acquired micro-CT data spanning from MIS 7 to MIS 3, as well as one Middle Pleistocene Homo specimen. Using the morphomap R routine [3], we evaluated the diaphyseal structure by using traditional cross-sectional properties and applied a 2D landmark-based geometric morphometric approach to delve into the endosteal, periosteal, and cross-sectional shape characteristics. These analyses were conducted at three distinct locations along the femoral diaphysis—subtrochanteric (80% of biomechanical length from the distal end), midshaft (50%), and mid-distal (35%). While conventional measurements of cross-sectional properties did not reveal clear trends among chronological and geographical groupings, multivariate analysis from the morphometric approach to cross-sectional shape allows us to define distinct clusters. Late Neanderthals of MIS 4 to 3 from Western and Northern Europe appear to differentiate from earlier specimens of Middle Pleistocene Homo and MIS 7 to 5 Neandertals. These differences result in Late Neandertals having more circular cross- sections in the proximal diaphysis and a medial buttress that is both more developed at midshaft and emerges from the mid-distal diaphysis. The present study therefore reveals clear chronological diversity in the structural patterns of Neanderthal femora. Few specimens from Northern Europe also exhibit deviations from the seemingly homogeneous pattern observed among Late Neanderthals, raising the possibility that these are idiosyncratic variations or regional differences.