Post-extubation dysphagia is well documented in the Intensive Care Unit (ICU) population, particularly following prolonged intubation (≥48 hours). Identifying patients with dysphagia is important as these individuals are more likely to develop pneumonia, and ICU patients who develop pneumonia are more likely to have poor outcomes. Despite the frequency and clinical significance of post-extubation dysphagia, there are currently no recognised, standard protocols outlining how and when to assess swallowing in patients after extubation. Assessing swallowing in this population is complicated by the high prevalence of silent aspiration, which cannot be identified on clinical assessment. Silent aspiration has been associated with attenuation of the cough reflex in the stroke population and cough reflex testing (CRT) has shown promise as a screening tool to identify patients who are at risk of silent aspiration. There is evidence in the literature that the cough reflex is impaired following short periods of orotracheal intubation for minor surgery, but the cough reflex has never been studied specifically in the post-extubation ICU population. Thus, it may be hypothesised that CRT is a suitable tool for assessing the cough reflex following extubation and may also be able to identify which patients are at the greatest risk of silent aspiration. This research programme investigated the impact of orotracheal intubation on the cough reflex. The goals of Study I were to identify and quantify impairment of the cough reflex following extubation and to track recovery of the cough reflex. Eighty-six participants who were admitted for elective coronary artery bypass grafting (CABG) underwent CRT prior to intubation using 0.4, 0.8 and 1.2 mol/L nebulised citric acid to establish baseline thresholds for reflexive cough. CRT was repeated within two hours of extubation to identify change from baseline cough. If a participant’s cough sensitivity was at their pre-intubation baseline, their participation in the study was complete. Participants who had an absent cough or required a stronger concentration of citric acid to stimulate cough were retested every morning and evening thereafter until they coughed at their baseline level, withdrew from the study or were discharged from hospital. Participants varied in time to recovery of cough reflex. Sixty percent of participants had an absent cough reflex at the first follow-up after extubation (M=70 minutes). By the fifth follow-up, which occurred at approximately 48 hours post-extubation, 86% of participants had recovered their baseline cough sensitivity. Age, gender and length of intubation had no significant impact on the time to recovery of cough reflex (p>0.3). There was a highly significant correlation between opioid dose and CRT result with participants with higher doses (mg/kg/hr) returning more quickly to baseline CRT. However, this was more likely due to the pattern of opioid administration, with patients passing the first CRT after extubation consistently having had higher recent opioid doses than patients passing on the fourth or fifth follow-up, rather than a causative relationship between high doses of opioids and increased cough sensitivity. The primary aim of Study II was to determine the sensitivity and specificity of CRT for identifying silent aspiration. One hundred and six ICU patients underwent CRT using 0.4, 0.6 and 0.8 mol/L nebulised citric acid and videoendoscopic evaluation of swallowing (VES) within 24 hours of extubation. Cough reflex threshold was established for each participant and cough responses were classified as strong or weak. VES was recorded for later evaluation by a speech-language therapist (SLT) who was blinded to the results of CRT. Thirty-nine (37%) participants had an absent cough to CRT. Thirteen (12%) participants aspirated on VES, 9 (69%) without a cough response. Sensitivity of CRT to identify silent aspiration was excellent at detecting both aspiration and silent aspiration at 0.4 and 0.6 mol/L nebulised citric acid, with weak cough responses grouped with absent responses. However, specificity of CRT to detect aspiration or silent aspiration was poor at all concentration and regardless of the grouping of weak cough responses with strong or weak responses. There was a significant correlation between intubation duration and presence of aspiration on VES (p=0.01). There was no significant correlation between silent aspiration on VES and length of intubation or either overt or silent aspiration and age, gender, reason for ICU admission, indication for intubation, APACHE III score, morphine equivalent dose or time of testing post-extubation. In summary, this research programme is the first to identify that cough reflex to citric acid is impaired following extubation and that this impairment often persists for up to 48 hours. It confirms that ICU patients are at risk of aspiration and silent aspiration following extubation, and provides new evidence that CRT has poor specificity when screening for silent aspiration risk in this population. This poor specificity suggests that the causes of post-extubation aspiration and post-extubation cough impairment differ. These results contribute to better understanding of post-extubation dysphagia. More research is needed to determine if CRT would be beneficial within particular patient groups after extubation and to determine the cause of post-extubation cough impairment.