In microvascular head and neck reconstruction, various factors such as diabetes, alcohol consumption, and preoperative radiation hold a risk for flap loss. The primary objective of this study was to examine the vessel morphology of both recipient and donor vessels and to identify predictors for changes in the diameters of H.E.-stained specimens associated with flap loss in a prospective setting. Artery and vein samples (N = 191) were collected from patients (N = 100), with sampling from the recipient vessels in the neck area and the donor vessels prior to anastomosis. External vessel diameter transverse (ED), inner vessel diameter transverse (ID), thickness vessel intima (TI), thickness vessel media (TM), thickness vessel wall (TVW), and intima-media ratio (IMR) for the recipient (R) and transplant site (T) in arteries (A) and veins (V) were evaluated using H.E. staining. Flap loss (3%) was associated with increased ARED (p = 0.004) and ARID (p = 0.004). Preoperative radiotherapy led to a significant reduction in the outer diameter of the recipient vein in the neck (p = 0.018). Alcohol consumption (p = 0.05), previous thrombosis (p = 0.007), and diabetes (p = 0.002) were associated with an increase in the total thickness of venous recipient veins in the neck. Diabetes was also found to be associated with dilation of the venous media in the neck vessels (p = 0.007). The presence of cardiovascular disease (CVD) was associated with reduced intimal thickness (p = 0.016) and increased total venous vessel wall thickness (p = 0.017) at the transplant site. Revision surgeries were linked to increased internal and external diameters of the graft artery (p = 0.04 and p = 0.003, respectively), while patients with flap loss showed significantly increased artery diameters (p = 0.004). At the transplant site, alcohol influenced the enlargement of arm artery diameters (p = 0.03) and the intima-media ratio in the radial forearm flap (p = 0.013). In the anterolateral thigh, CVD significantly increased the intimal thickness and the intima-media ratio of the graft artery (p = 0.01 and p = 0.02, respectively). Patients with myocardial infarction displayed increased thickness in the A. thyroidea and artery media (p = 0.003). Facial arteries exhibited larger total vessel diameters in patients with CVD (p = 0.03), while facial arteries in patients with previous thrombosis had larger diameters and thicker media (p = 0.01). The presence of diabetes was associated with a reduced intima-media ratio (p < 0.001). Although the presence of diabetes, irradiation, and cardiovascular disease causes changes in vessel thickness in connecting vessels, these alterations did not adversely affect the overall success of the flap.