Mucopolysaccharidosis IIIA (MPSIIIA) is a paediatric neurological lysosomal storage disease, characterised by a deficiency in the lysosomal hydrolase sulfo-glucosamine sulfo-hydrolase. This leads to the accumulation of partially degraded, highly sulphated heparan sulphate, resulting in widespread cellular and tissue dysfunction, predominantly in the CNS. Patients present with onset of symptoms early in the first decade of life, with progressive failure to achieve developmental milestones and severe behavioural changes, including hyperactivity, sleep disturbances and aggression. As the disease progresses, cognitive and later motor function decline ensue, with premature death in the second decade of life. There are no treatments currently available. Although we and others have previously focussed on delivering replacement enzyme, therapies targeting other aspects of childhood disease, notably abnormal behaviour and cognitive decline are warranted. Targeting brain inflammation represents a potential clinical intervention strategy. We set out to understand how disease pathology can lead to abnormal phenotypes, and particularly to understand if IL-1, a major pro-inflammatory mediator has a central role in neuroinflammation in MPSIIIA. MPSIIIA disease neuropathology involves multiple factors including heparan sulphate storage, storage of secondary substrates, and neuroinflammation. We first set out to unravel the role of storage substrates in inflammation. We demonstrated 2-O sulphation of MPSIIIA heparan sulphate was essential for inflammatory priming via the toll-like receptor 4/CD14/MD2 complex. In conjunction with heparan sulphate, MPSIIIA secondary storage substrates, cholesterol, amyloid beta and ATP activated the NLRP3 inflammasome and initiated secretion of IL-1beta in vitro. Using lentiviral-mediated haematopoietic stem cell gene therapy (HSCT) to drive human interleukin-1 receptor antagonist in a mouse model of MPSIIIA, we were able to attenuate the IL-1 immune response, which resulted in sustained reduced brain microgliosis and astrogliosis, and complete correction of hyperactivity and working memory defects. The contribution of IL-1 to abnormal behaviour associated with MPSIIIA was confirmed in a MPSIIIA x IL-1R1-/- mouse model. We compared two levels of human IL-1Ra overexpression via LV.IL1RN vector mediated HSCT in the MPSIIIA mouse model in order to determine whether there was a toxicity limit associated with IL-1Ra overexpression. We compared a maximal dose of LV.IL1RN against a lower dose of LV.IL1RN already known to be therapeutic and well tolerated. High dose LV.IL1RN HSCT demonstrated myelotoxicity, reduced leukocyte trafficking to the brain and liver and hyper-activation of resident immune cells. High dose LV.IL1RN HSCT was unable to correct the behavioural abnormalities associated with MPSIIIA. Lastly, we investigated the physician observation that MPSIII patients suffering from infection appear to deteriorate more rapidly post-recovery, with respect to cognitive decline. Several groups have documented stepwise declines in cognition following recovery from a systemic infection, in patients and animal models with Parkinsons disease, Amyotrophic lateral sclerosis, Alzheimers disease and Prion disease. We show that the viral mimetic poly(I:C) amplified sickness behavioural responses, exacerbated systemic and CNS cytokine expression, in particular IL-1beta and induced neuronal loss in MPSIIIA mice but not WT. We also showed that repeat poly(I:C) challenges in MPSIIIA animals exacerbated existing working memory deficits and hyperactive behaviour, and suggest that systemic infections represent a major risk factor for the progression of cognitive decline in MPSIIIA. Our findings indicate that IL-1 is a major driver of neuroinflammation and cognitive decline in MPSIIIA, and IL-1Ra is a potential anti-inflammatory therapeutic for neuro-inflammatory lysosomal diseases.