Lyme disease (LD) is the most common vector-borne disease in Ontario, Canada. We describe the epidemiology and clinical manifestations of LD in Ontario and examine trends in the incidence of non-disseminated and disseminated LD. LD surveillance data from the integrated Public Health Information System (iPHIS) from 2005-2014 were mapped to symptoms according to syndrome groups (erythema migrans (EM), flu-like, cardiac, neurologic or arthritic) and disease stages (early localized, early disseminated or late disseminated). During the study period, 1,230 cases due to Borrelia burgdoferi were reported in Ontario with annual incidence rates ranging from 0.32 (2006) to 2.16 (2013) cases per 100,000 population. Seventy percent of cases had EM and the proportion of cases with EM increased over time. Other clinical manifestations included flu-like (75%), arthritic (42%), neurologic (41%) and cardiac (6%) symptoms. Early localized disease (n = 415) manifested with EM (87%) and flu-like (57%) symptoms; early disseminated disease (n = 216) manifested with neurologic (94%), cardiac (10%) and EM (63%) symptoms; and late disseminated disease (n = 475) manifested with EM (62%), neurologic (55%), cardiac (9%), and arthritic symptoms (i.e., arthralgia (93%) and arthritis (7%)). Early localized and early disseminated cases (88% each) occurred primarily from May through September, compared to late disseminated cases (81%). The proportion of cases reported to public health within 30 days of illness onset increased during the study period, while the proportion of cases reported within 1-3 months and >3 months decreased. Geographical variations characterized by higher incidence of early localized disease and earlier public health notification (within 30 days of illness onset) occurred in regions with established or recently established LD risk areas, while later public health notification (>3 months after illness onset) was reported more frequently in regions with recently established or no identified risk areas. This is the first study to describe the clinical manifestations of LD in Ontario, Canada. The observed geographical variations in the epidemiology of LD in Ontario reinforce the need for regionally focused public health strategies aimed at increasing awareness, promoting earlier recognition and reporting, and encouraging greater uptake of preventive measures.