On the 29 September 1961, Nasser announced at a public rally that he would agree to the secession of Syria from the UAR. Admitting that maintaining the union would require the intervention of Egyptian troops, Nasser asserted that ‘Arab blood would not be shed by Arab hands’. Scholars would later observe that ‘with the exception of the Six-Day War this was the greatest setback of Nasser's political career’.

Political and intelligence assessments of the Syrian secession from the short-lived union have been largely neglected by historians. In fact, analysts demonstrated a long-standing awareness of the difficulties Nasser would face in Syria, although this fell short of outright prediction. They correctly identified the major obstacles to a successful union: the political domination of the regime in Cairo; military rivalry between the Egyptian and Syrian militaries; the role of the unpopular Syrian spy chief Abdul Hamid Sarraj; economic incompatibilities between Egypt and Syria; and contrasting political cultures between the two states. Yet somewhat derisive views of Syrian culture and positive perceptions of Nasser combined with the uncertainty of the secessionists themselves to impede prediction of an outright break-up.

Analysts were more astute in assessing the implications of secession. It is striking that despite fears in 1958 of an ‘expansionist’ Nasser absorbing Syria into an ever-growing Arab empire, the intelligence community was reluctant to welcome the break up and in fact regarded it as a potentially disruptive force, particularly in inter- Arab relations and the Arab–Israeli conflict. The Americans were particularly pessimistic about the prospect of a stable government emerging in Syria, perhaps reflecting an increasing sense of respect for Nasser. By 1961, the Egyptian President had come to be associated with ‘moderation’ and ‘stability’ in the region. As the American ambassador had predicted in 1958, the difficulty of realising the rhetorical ambitions of pan-Arab unity had nurtured a more reasonable and statesman-like Nasser. At the same time assessments perceptively warned policy-makers that such a severe setback to Nasser's pride or ‘honour’ might provoke an extreme reaction elsewhere.