By 1900, an average of five thousand people per day were processed through Ellis Island and doctors boasted an exam could be completed in six seconds. Questionnaires, filled out by passengers at their origination point, contained legal information and responses to twenty-nine questions. This document was used to cross-examine the new arrivals to assure their veracity and confirm their identity.
Only third-class passengers were herded into a small boat transporting them to Ellis Island. First- and second-class passengers were taken on a larger boat directly into New York Harbor and bypassed inspection at Ellis Island. Foreigners were directed to the main building where numbers were given to each passenger with directions to pin it onto their clothing. Confusion reigned as people from many different countries attempted to follow directions in a language completely foreign to them. Officers guided them into a daunting and immense red building. They were forced to leave their baggage in a room on the first floor and led upstairs to the Registry Room for medical and legal inspections. Without their knowledge, doctors watched the procession of immigrants as they climbed the staircase, looking for any excuse to refuse entrance into America (difficulty breathing, gait deformities, symptoms of disease, and/or abnormal behavior.) Once they arrived on the second floor, they were directed to one of twelve long queues, each separated by a long narrow bar. Anyone who failed the medical portion of their exam was marked with a variety of chalkmark designations ("X" for feeble-mindedness; "L" for lame, etc.) preventing their entry into the United States. Families were then forced to make one of two heartbreaking decisions: sending only relative(s) barred from U.S. entry back to their point of origin, or compelling the entire clan's return to their homeland.
This video from the Library of Congress shows a group of immigrants lined up to board a vessel leaving Ellis Island at the Immigration Depot.
A modern photo of the Great Hall of Ellis Island