Aspiration risk has a substantial influence on clinical management of swallowing disorders, and can be associated with pharyngeal residue. The aims of this cross-sectional study are to examine the correlation between the presence of pharyngeal residue and penetration-aspiration during fiberoptic endoscopic evaluation of swallowing (FEES), examine the correlation between objective data and Functional Oral Intake Scale (FOIS) and determine whether using objective assessment (Pooling score and Penetration Aspiration Scale-PAS) to categorise patients as pathological or not identifies the same patients identified by FOIS. Fifty-five patients with neurogenic dysphagia were evaluated during FEES by using the Pooling Score scale and PAS. They underwent an assessment of nutritional modalities using FOIS. There was a significant positive correlation between Pooling score and PAS scores for semisolid bolus (Pearson = 0.305; p = 0.024) and liquids (Pearson = 0.841; p = 0.000). The semi-solid bolus Pooling score had a negative correlation with FOIS (Pearson =- 0.355; p = 0.008), but there were no other significant correlations for FOIS with Pooling score or PAS. There were significant differences between objective assessments (P-score/PAS) and functional measure (FOIS) for identifying patients as pathological; although the positive predictive values were high, the negative predictive values were very low. Although pharyngeal residues are significantly associated with the presence of penetration-aspiration during endoscopy, the real intake modalities are not correlated with objective assessments of swallowing disorders. Therefore, clinicians need to implement a comprehensive approach to assess dysphagia.