Harris lines (HLs) are radiographically visible transverse lines of thickened bone that develop from temporary growth cessation during early life. Often attributed to physiological stress during development, HLs are frequently observed in the long bones of adolescents and become less visible over time due to bone remodeling. In recent years, the validity of HL as a sign of stress has been called into question and the methods used in studying HL through X-ray analysis scrutinized. In this study, 80 individuals from the Middle Holocene Cis-Baikal region of Siberia, from the Early Neolithic (EN; 7560–6660 HPD cal. BP) and Late Neolithic (LN; 6060–4970 HPD cal. BP), were studied for the presence and severity of HL. Radiographic analysis employed both the traditional clinical anteroposterior (A–P) orientation and a potentially improved mediolateral (M–L) orientation. EN groups in the Cis-Baikal are known to have experienced higher levels than their LN counterparts; thus, if HL reflect stress experiences, we expected to see more HL in the EN population compared with the LN population. We also expected more visible HL in the M–L orientation due to the suggested improvement in capturing more lines compared with the A–P orientation. While the results support the use of M–L orientation during X-ray capture of HL, there was not a higher number of HL in the EN population as expected. Instead, no significant differences were found in HL severity between the EN and LN populations, and age-at-death resulted in a greater effect on HL counts regardless of mortuary site. The results from this study align not with known stress data from the Middle Holocene Cis-Baikal populations but rather with data pertaining to known growth patterns. We therefore advocate against the use of HL as a sign of physiological stress and instead suggest HL as a reflection of bone growth trajectory.