A cross-sectional study combining different serological and molecular techniques for the detection of Ehrlichia species in dogs and their ticks was carried out with data from all regions of Costa Rica. A seroprevalence of 32.1% (131/408), and infection with E. canis of 3.2% (13/407) was found, whereas 6.9% (9/130) of ticks attached to the dogs were PCR positive to E. canis. Higher prevalences were found outside the Greater Metropolitan Area (GMA). Risk factors associated with E. canis seropositivity were age, between 2 and 7 years (RR: 1.6, 95% CI: 1.2–2.2) and 8–15 years (RR: 1.8, 95% CI: 1.2–3.0), number of dogs/total of households [Dogs per Household Ratio (DHR) ≥3.1 (RR: 2.0; 95% CI: 1.4–3.0)], number of dogs infested with at least one tick/total of dogs sampled [Tick Infestation Prevalence (TIP)≥31% (RR: 2.1; 95% CI:1.3–3.3)] and living outside the GMA (RR: 1.7; 95% CI: 1.2–2.4) and being a mixed-breed dog (RR: 1.5; 95% CI: 1.1–2.1). Risk factors for E. canis PCR positive dogs were a depressive attitude (OR: 11.2; 95% CI: 1.1–115.9), fever (OR:4.8; 95% CI:1.2–19.3), DHR≥3.1 (OR: 5.7; 95% CI:1.7–19.2)], number of ticks/total of dogs sampled [Tick Distribution Ratio (TDR) ≥2.1 (OR: 6.5; 95% CI: 1.3–31.8)], and TIP≥40% (OR: 5.7; 95% CI: 1.7–19.2). This paper describes E. canis seroprevalence, PCR prevalence and tick analysis in dogs from Costa Rica, with associated clinical signs and owner perceptions. In summary, most of the E. canis infections in dogs in our country seemed to pass unnoticed by owners. Since most of the seropositive dogs (97.7%, 131/134) were negative for E. canis DNA in their blood, it is important to determine in future studies if these dogs recovered from the E. canis infection without any medication, or are persistently infected, and will develop chronic disease.