Background <p>Severe leptospirosis often requires intensive care unit (ICU) treatment. The clinical phenotypes and outcomes of severe leptospirosis remain poorly characterised. We aimed to characterise the phenotypes and outcomes of patients with severe leptospirosis treated in the ICU.</p> Methods <p>We conducted a prospective cohort study at the Medical ICU of the National Hospital of Sri Lanka between January 2019 and January 2022 on adult patients with serologically or microbiologically confirmed leptospirosis. Clinical and laboratory data were recorded prospectively. Unsupervised two-step cluster analysis using six variables selected a priori (acute kidney injury, pulmonary haemorrhage, myocarditis, mechanical ventilation, renal replacement therapy, and hospital-acquired infections) was used to identify clinical phenotypes and to generate phenotypically distinct clusters of patients. Laboratory and biochemical parameters were compared across clusters. Kaplan–Meier survival analysis was used to compare mortality. The primary outcome was in-hospital mortality.</p> Results <p>One hundred and sixteen patients were included (mean age 43.9 years; males <i>n</i> = 103, 88.8%). Among them, 99.1% (<i>n</i> = 115) developed acute kidney injury, 62.1% (<i>n</i> = 72) developed pulmonary haemorrhage, and 75.9% (<i>n</i> = 88) developed myocarditis. Mechanical ventilation and dialysis were required in 56.9% (<i>n</i> = 66) and 75% (<i>n</i> = 87), respectively. Mortality rate was 17.2% (<i>n</i> = 20). Cluster analysis identified four phenotypes: (1) multi-organ failure (<i>n</i> = 43) (mortality of 25.6%, <i>n</i> = 11), (2) predominant respiratory failure (<i>n</i> = 20) (mortality of 35.0%, <i>n</i> = 7), (3) predominant renal failure (<i>n</i> = 26) (mortality of 7.7%, <i>n</i> = 2), and (4) intermediate severity (<i>n</i> = 27) (No mortality). Clusters with multi-organ and respiratory failure had higher hospital-acquired infection rates (<i>p</i> &lt; 0.001) and a longer ICU stay (<i>p</i> &lt; 0.001).</p> Conclusions <p>Critically ill patients with leptospirosis exhibit distinct clinical phenotypes with variable outcomes. Isolated pulmonary haemorrhage and multi-organ failure are associated with high mortality. These findings support the need for phenotype-based risk stratification, prognostication, and treatment.</p> Clinical trial registration <p>Not applicable.</p>