The years from 1890 to 1901 were difficult for Freud, but they were also some of the most productive years of his life. During this time he and Josef Breuer published the first psychoanalytic case studies (Studies on Hysteria, 1895), he completed his "self-analysis," and he wrote The Interpretation of Dreams, The Psychopathology of Everyday Life, and his case history Dora–all of which were to become classics.

In the early 1890s, Freud and Breuer frequently discussed their patients' cases with each other. At some point they decided to write up some of the more interesting cases for publication. Studies on Hysteria, published in 1895, was the result. The first case study presented in the book is by Breuer. In it, Breuer reports on his treatment of a patient (Bertha Pappenheim, called by the pseudonym "Anna O." in the book) who demonstrated many of the classic symptoms of hysteria. He treated her with the so-called "talking cure" or "cathartic cure," in which the patient discusses his or her associations with each of her symptoms and thereby causes them to disappear. Anna O.'s symptoms appeared to be associated with her father's illness. Anna O. was the first psychoanalytic patient. It was this new technique of talking through the patient's hidden memories that would become the center of Freud's technique. Freud believed that the hidden, or "repressed", memories that lay behind hysterical symptoms were always of a sexual nature. Breuer did not hold with this belief, which led to a split between the two men soon after the publication of the Studies.

Freud had met someone in November 1887 who would become his sole confidant and friend during his time of isolation in the 1890s. His name was Wilhelm Fliess, and he was a Berlin nose and throat doctor who had attended one of Freud's lectures at the University of Vienna on the recommendation of Josef Breuer. The two men soon started up a correspondence that lasted for some time. Each had his theories and thoughts to share with the other. Freud, convinced of the importance of sexuality for neurosis but shunned by his colleagues, found a supportive and eager audience in Fliess. Fliess–whose bizarre theories ranged from the existence of a "nasal neurosis" that could be cured by the application of cocaine to the nose, to a way of predicting when a woman would die based on the length of her menstrual period–found a similarly supportive, and much needed, audience in Freud. There were a great number of similarities between the men. Both held bizarre theories that were not supported by the medical mainstream; both were Jewish; and both had had a similar middle- class upbringing. Although their friendship fell apart in bitter disagreement around 1901, for the intervening years they were each other's strong supporters.

In October of 1896, Freud's father Jakob died. Freud later realized that this was the event that triggered his self-analysis during the next three years. Our record of Freud's self-analysis is based on the letters to Fliess and on the autobiographical and semi-autobiographical material in Freud's later writings. From 1897 to 1899, Freud dedicated himself to recording and analyzing his dreams, dredging up old childhood memories, and, in the process, determining the roots of his own neuroses. The dreams he had during this period provided much of the raw material for The Interpretation of Dreams, which was published in November 1899. During the course of his self-analysis Freud came to the conclusion that his own problems were due to a repressed desire for his mother and hostility towards his father. This was the famous "Oedipal complex" that became the heart of Freud's theory about the origin of neurosis in all of his patients.

When The Interpretation of Dreams was published, Freud had high hopes for it. Even toward the end of his career, he looked back on it as one of the best books he had written. But its reception was rather subdued: it sold a minimal number of copies and received a number of mixed reviews, many of which Freud either never saw or saw and forgot about. Freud was disappointed, but the middling sales did not keep him from working. He continued to treat patients, also finding the time to write The Psychopathology of Everyday Life, a book that proved to be somewhat more popular than The Interpretation of Dreams when it was published in 1901.

During this time, Freud's family life progressed more successfully than his career. We know very little about the married life of Sigmund and Martha Freud, because they no longer wrote letters to each other. From the little we can tell, however, they enjoyed a good marriage. Martha was never Freud's intellectual companion–her sister Minna Bernays fulfilled that function–but their relationship seems to have stayed healthy throughout their more than fifty years of marriage. Martha and Freud's first child, Mathilde, was born in 1887. She was followed by Anna, Martin, Sophie, Ernst, and Oliver.

Martin Freud has written an entertaining memoir of his childhood entitled Freud: Man and Father, in which he describes Freud as a reserved but loving father who worked extremely long hours but loved to spend days with his children during their summer vacations. Up until the time of the First World War, Freud and his family spent their summers away from Vienna, usually going to the mountains. Martha and the children would leave for vacation sometime in May, and Sigmund would follow in June or July. After spending a few weeks with the family, he would usually head off on a cultural vacation, often to Italy, and often with his brother Alexander.

It would be a mistake to consider this time of Freud's life completed isolated. He was indeed isolated from his professional colleagues, but he had a full social life. He joined the local B'nai B'rith, a Jewish social club, and he faithfully attended its bimonthly meetings for most of his life. On Sundays, he had the habit of playing a card game called tarok with a group of friends. And during the week, he frequently took long afternoon walks around Vienna with his older children.