When the Civil War started, the Krise family headed the Union Army's call for soldiers. Thomas's brothers Henry, Stephen, and Daniel; his brother-in-law Joshua Cretin and future brother-in-law Daniel Brand; and his nephews William H. Ryan and John Albert Nagle all fought for the Pennsylvania volunteers. Tragically, Joshua, William, and his brother Daniel all died in the War, and Henry returned him severely ill and died just a couple of years later.

While the War was raging, Thomas remained home on the farm. On August 24, 1864 he married Matilda "Tillie" Trexler, presumably at St. Augustine Catholic Church in St. Augustine. Tillie was born on January 29, 1841, the daughter of Peter and Ann Margaret (Donough) Trexler. Thomas's much older half-sister was married to Tillie's uncle Joseph Roy Trexler, and eight of Tillie's cousins were Thomas's nieces.

After witnessing the devastation the War wrought on his family, Thomas, who had not enlisted during the War's first four years, eventually enlisted (or perhaps was drafted?). He was mustered in on March 17, 1865 and served with Company M, 102nd Regiment of the Pennsylvania infantry. The war ended before he saw any action, and he was mustered out just three months later on June 28th.

He returned home just in time for the birth of their first child, Augustus James, who was born on July 27th.

Thomas and Tillie were eventually the parents of eleven children: Augustus James Krise, Anna Elizabeth Krise, Simon Linus Krise, Rose Mary (Krise) Fornwalt, Mary Margaret (Krise) Grove, Peter Silas Krise, Elmer Alfred Krise, Mary Elexena "Zena" (Krise) Conrad, Catherine Mary (Krise) McDermott, Thomas H. Krise, and Bennet Benjamin Krise.

Thomas and Tillie raised their children on their farm near St. Augustine in Clearfield Township.

When their son James was about six years old, he suffered a terrible cut on his left hand just above the wrist, which resulted from accidental play with an ax. It is thought that the wound healed and that he regained use of his hand.

Sadly, their second and third borns died young. Anna Elizabeth died in 1873 at the age of 5, and Simon Linus died in 1883 at the age of 14.

Thomas and Tillie both lived long lives. Their nine adult children produced at least 53 grandchildren and numerous more great-grandchildren.

On July 27, 1920 Thomas died at their home on St. Augustine Road, near St. Augustine. He was 79, and his death ended a marriage of almost 56 years.

Tillie died on June 26, 1937 at the home of their daughter in Altoona, Blair County. She was the grand old age of 96.

Thomas and Matilda had at least 53 grandchildren.