Peritoneal dialysis (PD) is a form of kidney replacement therapy that offers flexibility and autonomy to patients with end stage kidney disease. It is associated with lower costs compared to hemodialysis in many countries. Unlike mechanical complications that typical arise early in the course of treatment, non-infectious, non-mechanical complications often present late in patients that are established on PD. In this review, we first discuss abnormal-appearing drained dialysate, including hemoperitoneum, chyloperitoneum and non-infectious cloudy dialysate. The underlying cause is frequently unrelated to PD. We then discuss encapsulating peritoneal sclerosis, a rare complication of PD. Lastly, we review metabolic changes associated with PD, and methods to mitigate its effects.