Abstract Objective To analyze the association of neurological disorders (ND) and head and neck cancer (HNC) with dysphagia severity and aspiration pneumonia occurrence. Method Retrospective cohort study conducted at a university dysphagia center) for two consecutive years. Patients with ND or HNC were included if they had undergone a flexible endoscopic swallowing evaluation (FEES) at the dysphagia center, and at least one food consistency had been sampled and recorded. Outcomes of interest were swallowing safety, highest penetration-aspiration-score (PASmax), way of food intake, presence of a tracheal tube, and occurrence of pneumonia within the past two years. Results Of 257 consecutive patients, 199 were enrolled in the study and classified according to their underlying diagnosis into ND (120 patients) or HNC (79 patients). Forty-three HNC patients (54.4%) and 54 ND patients (45%) showed critical dysphagia in FEES (PAS ≥ 6). Binary logistic regression comparing both groups showed patients with ND to be 2.31 times more likely to develop pneumonia. However, if the 32 stroke patients were excluded from the calculation, PASmax remains the only significant variable affecting pneumonia risk in both groups. Liquids were the main challenge for ND patients, while aspirating HNC patients struggled with all consistencies. Conclusions The study shows that patients with HNC and ND differ in pneumonia risk only if stroke patients are included in the ND group. If they are excluded, the PAS score is the only remaining risk factor for pneumonia. Thickening liquids may not be suitable for all dysphagic patients; individually tailored measures might be more helpful, especially for HNC patients.