The aim of our study was to evaluate the role of morphogenetic variability in functional outcome of patients with ischemic stroke. The prospective study included 140 patients with acute ischemic stroke, all of whom were tested upon: admission; discharge; one month post-discharge; and three months post-discharge. The age was analyzed, as well. The Functional Independence Measure (FIM) test and the Barthel Index (BI) were used for the evaluation of functional outcomes for the eligible participants. We analyzed the presence of 19 homozygous recessive characteristics (HRC) in the studied individuals. There was a significant change in FIM values at discharge (p = 0.033) and in BI values upon admission (p = 0.012) with regards to the presence of different HRCs. Age significantly negatively correlated for the FIM score and BI values at discharge for the group with 5 HRCs (p < 0.05), while for BI only, negative significant correlation was noticed for the group with 5 HRCs at three months post-discharge (p < 0.05), and for the group with 3 HRCs at one month post-discharge (p < 0.05) and three months post-discharge (p < 0.05). Morphogenetic variability might be one among potentially numerous factors that could have an impact on the response to defined treatment protocols for neurologically-impaired individuals who suffered an ischemic stroke.