Blatter was born in the canton of Appenzell Innerrhoden in northeastern Switzerland in a region near Mount Säntis. Having lost his father at an early age, he was raised by an uncle, a popular doctor in the municipality of Rebstein in the neighboring Canton of St. Gallen. The young Blatter lived in his uncle's home, a castle overlooking Rebstein and located in the Rhine valley just before the river's union with Lake Constance (Bodensee). After finishing elementary education in Rebstein, Blatter attended middle school in Sarnen, the capital of the Canton of Obwalden, in Central Switzerland. His classmates at Sarnen remembered him as not only brilliant in every subject, but also a high-spirited companion with a reputation for pranks. After Sarnen, Blatter went on to have a brilliant career in high school in Schwyz, capital of the Canton of Schwyz, northeast of the canton of Obwalden. In October 1896, after finishing high school, Blatter moved to the border town of Feldkirch, Austria to join the Noviciate of the German Province of the Society of Jesus. Since German Jesuits were in exile under Bismarck, Blatter moved to the Netherlands in 1898 to first pursue classical studies and then study philosophy in the college of Valkenburg aan de Geul in the southernmost province of Limburg. Around this time, he also developed an interest in botany and attended many scientific conferences in Europe.