Neospora caninum infection is a major cause of abortion in dairy and beef cattle in many countries. Fast and accurate diagnosis of neosporosis is still the best disease control strategy. Thus, Np6 and Np21 primer sets were employed for the detection of N. caninum in the blood of 139 aborted cows and tissues of 25 foeti during a wave of abortion in five dairy farms in Egypt. The results revealed a 47.5% overall prevalence of N. caninum infection in aborted cows and a 64% overall prevalence in foeti. Two farms were PCR negative for the infection, and the other farms presented 45.7%, 87.0% and 90.9% molecular prevalence. The majority of PCR-positive foeti were aborted in the fifth month of pregnancy. The most common PCR-positive fetal tissue was the brain, followed by the heart, liver, stomach contents, and then the lung. The histopathological lesions in 5-month-old aborted foeti were microgliosis in the brain meninges and submeningially and myocarditis in heart tissue. At 7 months of abortion, multifocal necrosis, mononuclear cell infiltration, and neuron degeneration were observed in the brain. Heart tissue showed hemorrhage and necrotic changes. A tissue cyst was observed in the heart of 5-month aborted foeti and the brain of 7-month-old foeti. The sequenced amplicons from aborted cows and foeti were 100% identical to each other. As far as we are aware, our investigation is the first to sequence isolates of N. caninum from cattle hosts. The sequences were submitted to GenBank with the accession numbers OR939832.1 and PP708713.1. Multiple sequence alignments revealed variation between the study isolates and other published isolates from different regions and hosts. Phylogeny revealed clustering of our sequences with sequences of isolates from South Korea, China, and Italy. The sequences were distinct from sequences previously isolated from camels in Egypt.